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Xenbase Image ID: 153336

EDF 6. PSEUDOGENES
Illustration of htt.S pseudogene alignment to X. tropicalis htt, and the extant X. laevis htt.L, translated to amino acids. The amino acid position is shown at the beginning of each line. Missing codons are marked by ‘−’. Frameshifts and premature stops are marked by ‘X’ and ‘*’ respectively (and pointed to with red arrows). (top) the first exon of the pseudogene is completely missing from the S chromosome. The characteristic poly-Q region is maintained by both htt and htt.L. (bottom) An exon with conservation in the pseudogene, illustrating that despite many frameshifts, premature stops, and the lack of a proper start, and insertions of new sequence, we identify many codons in the pseudogene that occur in large conserved blocks.Illustration of our model to compute pseudogene ages. The star represents the point of nonfunctionalization for a currently pseudogenized locus. We assume the expected rate of nonsynonymous changes can be estimated by the Ka of the extant gene and X. tropicalis. We then compare the Ks and Ka of the pseudogene sequence to estimate the time of nonfunctionalization. See Supplemental Note 9 for a more detailed discussion.Estimated epochs of pseudogenization for 430 genes are indistinguishable from a burst of pseudogenization > 10 Mya (Ks > 0.03). See Supplemental Note 9 for a more detailed discussion.Correlation of pseudogene expression with its extant homeolog. The little expression seen in pseudogenes tends to be uncorrelated with the extant homeolog.Histogram of pseudogene expression values across all 28 tissues and developmental stages (red) compared to all extant genes (blue). The pseudogenes are rarely expressed, and tend to be expressed at lower levels than extant protein-coding genes.Histograms of expression variance of pseudogenes (red) compared to extant genes (blue). The small amount of pseudogene expression observed does not tend to vary across tissues and developmental stages in the same way that extant genes do.